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-1
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0answers
18 views

glibc double free or corruption error when running Oases transcriptome assembler. [closed]

Trying to merge assemblies for a set of noncoding RNA but I am getting . I compiled Oases and Velvet such that "MAXKMERLENGTH=101" (kmer steps from 61 to 101 with 4-step increments) and ...
0
votes
1answer
27 views

What does the “cov” mean in a velvet assembler generated contig name?

A exmaple of a contig name generated by velvet assembler: NODE_127_length_39203_cov_244.873016 What does cov_244.873016 mean? ...
1
vote
1answer
57 views

How Scientists sequence, assemble and annotate plant genomes? [closed]

I previously read this question and this paper and learned good things about this topic. my current question is that scientists use which tools, algorithms, soft wares... to sequence, assemble and ...
4
votes
0answers
39 views

Which sequence assemblers I can use to compare different paradigms?

I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (Greedy, OLC, De Bruijn). I ...
3
votes
0answers
27 views

Gibson assembly - primer design with A and T rich regions

I have question about Gibson assembly. I have done it several times and it always worked okay for us, but now I want to assemble together a fragment which has sequence like this: ...
2
votes
0answers
34 views

Assembly reconciliation

We have some bacterial genomes that were assembled using Spades, they were sequenced with and IonTorrent PGM. There are many assemblers and they give different results. I was interested in a tool ...
4
votes
2answers
484 views

Why is assembling paired end illumina without any input parameters an important problem?

In one of the comments in this question about multiple sequence alignment, it was stated @5heikki: btw if you want a good bioinformatics problem, come up with an assembler that assembles any ...
1
vote
0answers
127 views

Is the default kmer 25 value in Trinity still ok for assembly of 150bp reads from Illumina HiSeq 2500?

I will soon be receiving Illumina HiSeq 2500 data (150bp PE stranded reads). In the past we have been using Trinity as our assembler of choice, but it uses a default kmer value of 25. I believe this ...
5
votes
3answers
202 views

How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: ...
38
votes
4answers
2k views

What exactly are computers used for in DNA sequencing?

I've thoroughly read the Wikipedia article on DNA sequencing and can't get one thing. There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts. ...